Man page - gt-readjoiner-prefilter(1)
Packages contains this manual
- gt-readjoiner(1)
- gt-cds(1)
- gt-extractfeat(1)
- gt-dupfeat(1)
- gt-select(1)
- gt-encseq(1)
- gt-matstat(1)
- gt-md5_to_id(1)
- gt-seqmutate(1)
- gt-seqtranslate(1)
- gt-mkfeatureindex(1)
- gt-dot(1)
- gt-compreads-decompress(1)
- gt-compreads-refcompress(1)
- gt-condenseq(1)
- gt-readjoiner-prefilter(1)
- gt-seqstat(1)
- gt-readjoiner-overlap(1)
- gt-splicesiteinfo(1)
- gt-prebwt(1)
- gt-extractseq(1)
- gt-encseq2spm(1)
- gt-convertseq(1)
- gt-clean(1)
- gt-encseq-encode(1)
- gt-ltrclustering(1)
- gt-seq(1)
- gt-ltrharvest(1)
- gt-sequniq(1)
- gt-inlineseq_split(1)
- gt-mergefeat(1)
- gt-splitfasta(1)
- gt-gtf_to_gff3(1)
- gt-ltrdigest(1)
- gt-seqfilter(1)
- gt-featureindex(1)
- gt-inlineseq_add(1)
- gt-speck(1)
- gt-mmapandread(1)
- gt-tallymer-mkindex(1)
- gt-seed_extend(1)
- gt-hop(1)
- gt-sketch(1)
- gt-repfind(1)
- gt-shulengthdist(1)
- gt-sketch_page(1)
- gt-gff3(1)
- gt-stat(1)
- gt-gff3validator(1)
- gt-packedindex(1)
- gt-merge(1)
- gt-wtree(1)
- gt-encseq-bitextract(1)
- gt-seqids(1)
- gt-readjoiner-assembly(1)
- gt-tirvish(1)
- gt-uniquesub(1)
- gt-encseq-sample(1)
- gt-chseqids(1)
- gt-compreads-compress(1)
- gt-scriptfilter(1)
- gt-seqtransform(1)
- gt-eval(1)
- gt-genomediff(1)
- gt-congruence(1)
- gt-chain2dim(1)
- gt-tallymer(1)
- gt-tagerator(1)
- gt-loccheck(1)
- gt-encseq-info(1)
- gt-snpper(1)
- gt-bed_to_gff3(1)
- gt(1)
- gt-matchtool(1)
- gt-simreads(1)
- gt-csa(1)
- gt-tallymer-occratio(1)
- gt-encseq-check(1)
- gt-tallymer-search(1)
- gt-encseq-bench(1)
- gt-shredder(1)
- gt-gff3_to_gtf(1)
- gt-orffinder(1)
- gt-encseq-decode(1)
- gt-compreads(1)
- gt-encseq-md5(1)
- gt-uniq(1)
- gt-congruence-spacedseed(1)
- gt-id_to_md5(1)
- gt-seqorder(1)
- gt-compreads-refdecompress(1)
- gt-fingerprint(1)
- gt-fastq_sample(1)
- gt-interfeat(1)
apt-get install genometools
Manual
GT-READJOINER-PREF
NAMESYNOPSIS
DESCRIPTION
REPORTING BUGS
NAME
gt-readjoiner-prefilter - Remove contained and low-quality reads and encode read set in GtEncseq format.
SYNOPSIS
gt readjoiner prefilter [option ...]
DESCRIPTION
-readset [ string ]
specify the readset name default: filename of first input sequence_file
-db
specify a list of input libraries (Fasta/FastQ); for single-end libraries use the filename (which is not allowed to contain : symbols); for paired-end libraries with reads interleaved (f,r,f,r,...) in a single file use the notation <filename>:<insertlength>[,<stdev>] (stdev may be omitted); for paired-end with reads in two files (f, r) use the notation <file_f>:<file_r>:<insertlength>[,<stdev>]
-v [ yes|no ]
be verbose (default: no)
-q [ yes|no ]
suppress standard output messages (default: no)
-des [ yes|no ]
store Fasta IDs (or entire descriptionsif used together with -clipdes no) warning: increases the memory requirement (default: no)
-clipdes [ yes|no ]
clip Fasta descriptions after first space set to false if you need entire descriptions (default: yes)
-memdes [ yes|no ]
use memory storage for descriptions (default: use temporary disk storage)
-maxlow [ value ]
maximal number of low-quality positions in a read default: infinite
-lowqual [ value ]
maximal quality for a position to be considered low-quality (default: 3)
-phred64 [ yes|no ]
use phred64 scores for FastQ format (default: no)
-help
display help for basic options and exit
-help+
display help for all options and exit
-version
display version information and exit
REPORTING BUGS
Report bugs to https://github.com/genometools/genometools/issues.